Nimmo, Rachael A. et al. (2009) International Worm Meeting "The Tip60-p400 chromatin remodeling complex promotes maintenance of the undifferentiated state in C. elegans seam stem cells by inhibiting let-7-dependent terminal differentiation."

Nimmo, Rachael A., Slack, Frank J.

[International Worm Meeting, 2009]

The Tip60-p400 chromatin remodeling and histone acetyl-transferase complex is recruited to both active and inactive promoters in embryonic stem (ES) cells to maintain the undifferentiated stem cell fate. We have discovered that in C. elegans, ssl-1 (p400)or mys-1 (Tip60) knockdown causes the seam stem cells to partially differentiate early. In addition, ssl-1 RNAi enhances the precocious terminal differentiation exhibited by lin-14 mutants and partially suppresses retarded seam cell defects in let-7 mutants, indicating that ssl-1 may be regulating,or be regulated by, let-7 family miRNAs. We are currently investigating how ssl-1 and mys-1 promote the undifferentiated state and regulate the timing of terminal differentiation of the seam cells. It is known that Tip60-p400 complexes are recruited to H3K4me3 marks in ES cells in a Nanog-dependent manner and regulate transcription of important stem cell genes. LIN-28 is an important stemness factor, and is highly expressed in undifferentiated ES cells and worm seam stem cells, but is downregulated prior to differentiation. LIN-28 inhibits let-7 processing in ES cells and in C. elegans lin-28 and let-7 are important members of the heterochronic pathway regulating developmental timing. Terminal differentiation of the seam cells occurs precociously in lin-28 mutants but is delayed in let-7 mutants, therefore LIN-28 and let-7 act in opposing ways to regulate the balance between proliferation and differentiation. In mammals, Myc recruits Tip60-p400 to promoters in order to promote cell proliferation and Myc inhibits let-7 via transactivation of lin-28. Therefore we are investigating whether the Tip60-p400 HAT complex promotes maintenance of the undifferentiated fate by inhibiting let-7 family miRNAs through upregulation of LIN-28, as well as how Tip60-p400 genes interact with other heterochronic genes such as lin-41 and hbl-1. Interestingly, Tip60 is known to interact with both the Amyloid Precursor Protein (APP) Intracellular Domain (AICD) and the Notch Intracellular domain (NICD) and in C. elegans both apl-1 (APP) and lin-12(Notch) have been found to regulate the timing of terminal differentiation of the seam stem cells, consistent with evidence from mammalian studies suggesting that the NICD disrupts AICD-Tip60 complex formation and that Tip60 is required for the intracellular signaling role of APP. We are therefore investigating whether MYS-1, LIN-12 and APL-1 interact in C.elegans and how chromatin remodeling may participate in Notch and APP signaling in the temporal regulation of terminal differentiation in seam stem cells.

McGhee JD (1987) Biochemistry "Purification and characterization of a carboxylesterase from the intestine of the nematode Caenorhabditis elegans."

McGhee JD

[Biochemistry, 1987]

The major intestinal esterase from the nematode Caenorhabditis elegans has been purified to essential homogeneity. Starting from whole worms, the overall purification is 9000-fold with a 10% recovery of activity. The esterase is a single polypeptide chain of Mr 60,000 and is stoichiometrically inhibited by organophosphates. Substrate preferences and inhibition patterns classify the enzyme as a carboxylesterase (EC 3.1.1.1), but the physiological function is unknown. The sequence of 13 amino acid residues at the esterase N- terminus has been determined. This partial sequence shows a surprisingly high degree of similarity to the N-terminal sequence of two carboxylesterases recently isolated from Drosophila mojavensis [Pen, J., van Beeumen, J., & Beintema, J. J. (1986) Biochem. J. 238, 691-699].

Murakami S et al. (1999) Curr Biol "Life extension and stress resistance in Caenorhabditis elegans modulated by the tkr-1 gene."

Johnson TE, Murakami S

[Curr Biol, 1999]

In this Brief Communication, which appeared in the 14 September 1998 issue of Current Biology, the UV dose was reported erroneously. The dose reported was 20 J/m2 but the actual dose used was 0.4 J/cm2. Also, the gene formally referred to as tkr-1 has since been renamed old-1 (overexpression longevity determination).

Ramos CG et al. (2014) J Bacteriol "Retraction for Ramos et al., MtvR is a global small noncoding regulatory RNA in Burkholderia cenocepacia."

Feliciano JR, da Costa PJ, Ramos CG, Grilo AM, Leitao JH

[J Bacteriol, 2014]

Volume 195, no. 16, p. 35143523, 2013. A number of problems related to images published in this paper have been brought to our attention. Figure 1D contains duplicated images in lanes S and LE, and Fig. 4D and 6B contain images previously published in articles in this journal and in Microbiology and Microbial Pathogenesis, i.e., the following: C. G. Ramos, S. A. Sousa, A. M. Grilo, J. R. Feliciano, and J. H. Leitao, J. Bacteriol. 193:15151526, 2011. doi:10.1128/JB.01374-11. S. A. Sousa, C. G. Ramos, L. M. Moreira, and J. H. Leitao, Microbiology 156:896908, 2010. doi:10.1099/mic.0.035139-0. C. G. Ramos, S. A. Sousa, A. M. Grilo, L. Eberl, and J. H. Leitao, Microb. Pathog. 48:168177, 2010. doi: 10.1016/j.micpath.2010.02.006. Therefore, we retract the paper. We deeply regret this situation and apologize for any inconvenience to the editors and readers of Journal of Bacteriology, Microbial Pathogenesis, and Microbiology.

Nillegoda NB et al. (2015) Nature "Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation."

Berynskyy M, Morimoto RI, Bukau B, Stengel F, Kirstein J, Szlachcic A, Arnsburg K, Stank A, Scior A, Nillegoda NB, Gao X, Guilbride DL, Aebersold R, Wade RC, Mayer MP

[Nature, 2015]

Protein aggregates are the hallmark of stressed and ageing cells, and characterize several pathophysiological states. Healthy metazoan cells effectively eliminate intracellular protein aggregates, indicating that efficient disaggregation and/or degradation mechanisms exist. However, metazoans lack the key heat-shock protein disaggregase HSP100 of non-metazoan HSP70-dependent protein disaggregation systems, and the human HSP70 system alone, even with the crucial HSP110 nucleotide exchange factor, has poor disaggregation activity in vitro. This unresolved conundrum is central to protein quality control biology. Here we show that synergic cooperation between complexed J-protein co-chaperones of classes A and B unleashes highly efficient protein disaggregation activity in human and nematode HSP70 systems. Metazoan mixed-class J-protein complexes are transient, involve complementary charged regions conserved in the J-domains and carboxy-terminal domains of each J-protein class, and are flexible with respect to subunit composition. Complex formation allows J-proteins to initiate transient higher order chaperone structures involving HSP70 and interacting nucleotide exchange factors. A network of cooperative class A and B J-protein interactions therefore provides the metazoan HSP70 machinery with powerful, flexible, and finely regulatable disaggregase activity and a further level of regulation crucial for cellular protein quality control.

Miller DM et al. (1992) Worm Breeder's Gazette "unc-4 LacZ Expression in A-Type Motor Neurons"

Miller DM, Niemeyer CJ

[Worm Breeder's Gazette, 1992]

unc-4 LacZ expression in A-type motor neurons David M. Miller and Charles J. Niemeyer, Dept. of Cell Biology, Duke Univ. Medical Ctr, Durham, NC 27710

C Hammell et al. (2007) International Worm Meeting "NHL-2, a predicted E3 ubiquitin ligase, functions with the let-7 family microRNAs in hbl-1 regulation."

Victor Ambros, C Hammell

[International Worm Meeting, 2007]

The coordination of developmental timing requires the concerted action of both protein products and several small, regulatory RNAs that control their expression. A classical example of this type of regulation revolves around the negative regulation of lin-41 by the microRNA let-7 via complementary binding of this small RNA to the lin-41 3UTR(1). lin-41 encodes a putative E3 ubiquitin ligase and is a founding member of a small family of predicted C. elegans E3 ligases called the RBBC-NHL family (including nhl-1, nhl-2, and nhl-3)(2, 3). In this report, we identify nhl-2 as a component of the heterochronic regulatory pathway that functions in parallel to lin-46 and daf-12 to repress L2 specific cell fate programs to the second larval stage. nhl-2 also functions in concert with the let-7 family of microRNAs (mir-241, mir-48, and mir-84) to properly regulate hbl-1 expression via the hbl-1 3UTR (4) and suggests an intimate interplay between two seemingly divergent forms of post-transcriptional regulation. Consistent with this coupling occurring at the molecular level, we also find that NHL-2 physically associates with ALG-1 and ALG-2, the C. elegans microRNA specific Argonautes. The coupling of nhl-2 activity to let-7 family microRNA function appears to be specific for hbl-1 down-regulation as nhl-2 is dispensable for the regulation of other targets of let-7 family members (including let-60 and lin-41). We will also present evidence that the type of physical and genetic interactions between other RBBC-NHL family members (including LIN-41 and NHL-1), ALG-1/2 and other particular microRNA families/targets are similar to the relationships shared between nhl-2, the let-7 family of microRNAs and hbl-1. 1.B. J. Reinhart et al., Nature 403, 901 (2000). 2.F. J. Slack et al., Mol Cell 5, 659 (Apr, 2000). 3.F. J. Slack, G. Ruvkun, Trends Biochem Sci 23, 474 (Dec, 1998). 4.A. L. Abbott et al., Dev Cell 9, 403 (Sep, 2005).

Sommer RJ et al. (1994) Worm Breeder's Gazette "Evolution of Vulva-Formation: Part II: Species With a Central Vulva"

Sommer RJ, Sternberg PW

[Worm Breeder's Gazette, 1994]

Evolution of vulva-formation: Part II: Species with a central vulva Ralf J. Sommer & Paul W. Sternberg, California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125

Jun-ichi Aikawa (2001) International C. elegans Meeting "Molecular characterization of heparan sulfate/heparin N-deacetylase/N-sulfotransferase in worms"

Jun-ichi Aikawa

[International C. elegans Meeting, 2001]

Heparan sulfate binds and activates a large variety of growth factors, enzymes and extracellular matrix proteins. These interactions largely depend on the specific arrangement of sulfated moieties and uronic acid epimers within the chains. These oligosaccharide sequences are generated in a step-wise manner, initiated by the formation of a linkage tetrasaccharide which is then extended by copolymerization of alternating a1,4GlcNAc and b1,4GlcA residues. As the chains polymerize, they undergo a series of sulfation and epimerization reactions. The first set of modifications involves the removal of acetyl units from subsets of GlcNAc residues, and the addition of sulfate groups to the resulting free amino groups. These reactions are catalyzed by a family of enzymes designated as GlcNAc N-deacetylase/N-sulfotransferases (NDST), since they simultaneously. Four members of the family have been identified in vertebrates, with single orthologs present in Drosophila and C. elegans. We have revealed tissue-specific expression pattern and unique enzymatic properties of these four isozymes1,2). In fly, loss of NDST (sulfateless) results in unsulfated chains and defective signaling by multiple growth factors and morphogens. I reconstituted cDNA for worm NDST from EST clones and 5' RACE products. Enzymatic activities will be discussed. 1) Aikawa, J. & Esko, J. D J. Biol. Chem. 274, 2690-2695 (1999) 2) Aikawa, J., Grobe, K., Tsujimoto, M. & Esko, J. D J. Biol. Chem. 276, 5876-5882 (2001)

Dreyfus DH et al. (1999) Mol Immunol "Comparative analysis of invertebrate Tc6 sequences that resemble the vertebrate V(D)J recombination signal sequences (RSS)."

Gelfand EW, Dreyfus DH

[Mol Immunol, 1999]

Invertebrate cells lack the p53 recombination checkpoint but contain mobile DNA sequences that transpose by a mechanism in part shared with excision of the V(D)J recombination signal sequences (RSS). In this work, inversion, deletion, and duplication of sequences associated with an invertebrate C. elegans Tc6 element is described. The structure of this C. elegans sequence and other dispersed Tc6 elements suggests that covalently closed 'hairpin' structures are not unique to excision of the V(D)J RSS by the RAG proteins, but rather can be generated by transposases at transposon termini leading to characteristic inversion and duplication events. Comparative analysis of recombination events at invertebrate sequences resembling the vertebrate V(D)J RSS may be useful in understanding V(D)J recombination-mediated recombination events in malignant vertebrate cells or genetic diseases such as ataxia telangectasia, in which the p53 recombination checkpoint is defective.